The foreign ministry in Moscow said it was giving Estonia's consul in the second city of Saint Petersburg and another diplomat in the city of Pskov five days to quit the country.
The ministry slammed the "destructive line" of the Estonian authorities and insisted that Tallinn was responsible for the harm done to bilateral ties.
Estonia's foreign ministry said Friday it had expelled two Russian diplomats, in the latest incident to strain relations between the small NATO member state and Moscow.
Relations between Moscow and Tallinn have been fraught since Estonia broke free from the crumbling Soviet Union in 1991, joining both the EU and NATO in 2004.
NATO is currently deploying four battalions to the three Baltic states -- Estonia, Latvia and Lithuania -- and Poland to reassure its allies spooked by Russia's 2014 annexation of Crimea from Ukraine.
Moscow today also expelled five Moldovan diplomats in a tit-for-tat move after the tiny ex-Soviet country slung out its officials.
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